Voronoi-Based Segmentation of Cells on Image Manifolds. - Thouis R. Jones; Anne E. Carpenter; Polina Golland (CVBIA, 2005)

CellProfiler Analyst: data exploration and analysis software for complex image-based screens. - Thouis R. Jones; In Han Kang; Douglas B. Wheeler; Robert A. Lindquist; Adam Papallo; David M. Sabatini; Polina Golland; Anne E. Carpenter (BMC Bioinform., 2008)

Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution. - Björn Nilsson; Mikael Johansson; Fátima Al-Shahrour; Anne E. Carpenter; Benjamin L. Ebert (Bioinform., 2009)

Introduction to the Quantitative Analysis of Two-Dimensional Fluorescence Microscopy Images for Cell-Based Screening. - Vebjorn Ljosa; Anne E. Carpenter (PLoS Comput. Biol., 2009)

Resolving clustered worms via probabilistic shape models. - Carolina Wählby; Tammy Riklin-Raviv; Vebjorn Ljosa; Annie L. Conery; Polina Golland; Frederick M. Ausubel; Anne E. Carpenter (ISBI, 2010)

Morphology-Guided Graph Search for Untangling Objects: C. elegans Analysis. - Tammy Riklin Raviv; Vebjorn Ljosa; Annie L. Conery; Frederick M. Ausubel; Anne E. Carpenter; Polina Golland; Carolina Wählby (MICCAI (3), 2010)

Towards automated high-throughput screening of C. elegans on agar - Mayank Kabra; Annie L. Conery; Eyleen J. O'Rourke; Xin Xie; Vebjorn Ljosa; Thouis R. Jones; Frederick M. Ausubel; Gary Ruvkun; Anne E. Carpenter; Yoav Freund (CoRR, 2010)

Extracting biomedically important information from large, automated imaging experiments. - Anne E. Carpenter (ISBI, 2011)

Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software. - Lee Kamentsky; Thouis R. Jones; Adam Fraser; Mark-Anthony Bray; David J. Logan; Katherine L. Madden; Vebjorn Ljosa; Curtis Rueden; Kevin W. Eliceiri; Anne E. Carpenter (Bioinform., 2011)

Visualization of Parameter Space for Image Analysis. - A. Johannes Pretorius; Mark-Anthony Bray; Anne E. Carpenter; Roy A. Ruddle (IEEE Trans. Vis. Comput. Graph., 2011)

Behavior in the Time of Cholera: Evidence from the 2008-2009 Cholera Outbreak in Zimbabwe. - Anne E. Carpenter (SBP, 2014)

ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments. - Imtiaz A. Khan; Adam Fraser; Mark-Anthony Bray; Paul J. Smith; Nick S. White; Anne E. Carpenter; Rachel J. Errington (Bioinform., 2014)

Symmetry-based mitosis detection in time-lapse microscopy. - Topaz Gilad; Mark-Anthony Bray; Anne E. Carpenter; Tammy Riklin Raviv (ISBI, 2015)

Analysis of High-throughput Microscopy Videos: Catching Up with Cell Dynamics. - Assaf Arbelle; N. Drayman; Mark-Anthony Bray; U. Alon; Anne E. Carpenter; Tammy Riklin Raviv (MICCAI (3), 2015)

CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data. - Mark-Anthony Bray; Anne E. Carpenter (BMC Bioinform., 2015)

CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets. - David Dao; Adam Fraser; Jane Hung; Vebjorn Ljosa; Shantanu Singh; Anne E. Carpenter (Bioinform., 2016)

CP-CHARM: segmentation-free image classification made accessible. - Virginie Uhlmann; Shantanu Singh; Anne E. Carpenter (BMC Bioinform., 2016)

QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni. - Cleber C. Melo-Filho; Rafael Ferreira Dantas; Rodolpho C. Braga; Bruno Junior Neves; Mario R. Senger; Walter C. G. Valente; João M. Rezende-Neto; Willian T. Chaves; Eugene N. Muratov; Ross A. Paveley; Nicholas Furnham; Lee Kamentsky; et al. (J. Chem. Inf. Model., 2016)

Applying Faster R-CNN for Object Detection on Malaria Images. - Jane Hung; Anne E. Carpenter (CVPR Workshops, 2017)

Weakly Supervised Learning of Single-Cell Feature Embeddings. - Juan C. Caicedo; Claire McQuin; Allen Goodman; Shantanu Singh; Anne E. Carpenter (CVPR, 2018)

Combining morphological and migration profiles of in vitro time-lapse data. - Tim Becker; Juan C. Caicedo; Shantanu Singh; Markus Weckmann; Anne E. Carpenter (ISBI, 2018)

Applying Faster R-CNN for Object Detection on Malaria Images. - Jane Hung; Allen Goodman; Stefanie Lopes; Gabriel Rangel; Deepali Ravel; Fabio T. M. Costa; Manoj Duraisingh; Matthias Marti; Anne E. Carpenter (CoRR, 2018)

Capturing Single-Cell Phenotypic Variation via Unsupervised Representation Learning. - Maxime W. Lafarge; Juan C. Caicedo; Anne E. Carpenter; Josien P. W. Pluim; Shantanu Singh; Mitko Veta (MIDL, 2019)

DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images. - Victor Kulikov; Syuan-Ming Guo; Matthew Stone; Allen Goodman; Anne E. Carpenter; Mark Bathe; Victor S. Lempitsky (PLoS Comput. Biol., 2019)

Keras R-CNN: library for cell detection in biological images using deep neural networks. - Jane Hung; Allen Goodman; Deepali Ravel; Stefanie Lopes; Gabriel Rangel; Odailton A. Nery; Benoit Malleret; Francois Nosten; Marcus V. G. Lacerda; Marcelo U. Ferreira; Laurent Rénia; Manoj Duraisingh; et al. (BMC Bioinform., 2020)

Bridging Domain and Data. - Anne E. Carpenter (Patterns, 2020)

CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis. - David R. Stirling; Anne E. Carpenter; Beth A. Cimini (Bioinform., 2021)

CellProfiler 4: improvements in speed, utility and usability. - David R. Stirling; Madison J. Swain-Bowden; Alice M. Lucas; Anne E. Carpenter; Beth A. Cimini; Allen Goodman (BMC Bioinform., 2021)

A field guide to cultivating computational biology. - Anne E. Carpenter; Casey S. Greene; Piero Carnici; Benilton S. Carvalho; Michiel de Hoon; Stacey D. Finley; Kim-Anh Lê Cao; Jerry S. H. Lee; Luigi Marchionni; Suzanne Sindi; Fabian J. Theis; Gregory P. Way; et al. (CoRR, 2021)

Developing open-source software for bioimage analysis: opportunities and challenges. - Florian Levet; Anne E. Carpenter; Kevin W. Eliceiri; Anna Kreshuk; Peter Bankhead; Robert Haase 001 (F1000Research, 2021)

Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic. - Yuen Ler Chow; Shantanu Singh; Anne E. Carpenter; Gregory P. Way (PLoS Comput. Biol., 2022)

Pseudo-Labeling Enhanced by Privileged Information and Its Application to In Situ Sequencing Images. - Marzieh Haghighi; Mario C. Cruz; Erin Weisbart; Beth A. Cimini; Avtar Singh; Julia Bauman; Maria E. Lozada; Sanam L. Kavari; James T. Neal; Paul C. Blainey; Anne E. Carpenter; Shantanu Singh (IJCAI, 2023)

MOTIVE: A Drug-Target Interaction Graph For Inductive Link Prediction. - John Arevalo; Ellen Su; Anne E. Carpenter; Shantanu Singh (NeurIPS, 2024)

MOTIVE: A Drug-Target Interaction Graph For Inductive Link Prediction. - John Arevalo; Ellen Su; Anne E. Carpenter; Shantanu Singh (CoRR, 2024)

Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning. - Robert van Dijk; John Arevalo; Mehrtash Babadi; Anne E. Carpenter; Shantanu Singh (PLoS Comput. Biol., 2024)

Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank. - Srijit Seal; Ola Spjuth; Layla Hosseini-Gerami; Miguel García-Ortegón; Shantanu Singh; Andreas Bender 002; Anne E. Carpenter (J. Chem. Inf. Model., 2024)

Learning Molecular Representation in a Cell. - Gang Liu 025; Srijit Seal; John Arevalo; Zhenwen Liang; Anne E. Carpenter; Meng Jiang 001; Shantanu Singh (ICLR, 2025)

MorphoDiff: Cellular Morphology Painting with Diffusion Models. - Zeinab Navidi; Jun Ma 016; Esteban Miglietta; Le Liu; Anne E. Carpenter; Beth A. Cimini; Benjamin Haibe-Kains; Bo Wang 044 (ICLR, 2025)

cp_measure: API-first feature extraction for image-based profiling workflows. - Alán F. Muñoz; Tim Treis; Alexandr A. Kalinin; Shatavisha Dasgupta; Fabian J. Theis; Anne E. Carpenter; Shantanu Singh (CoRR, 2025)

Foreground-aware Virtual Staining for Accurate 3D Cell Morphological Profiling. - Alexandr A. Kalinin; Paula Llanos; Theresa Maria Sommer; Giovanni Sestini; Xinhai Hou; Jonathan Z. Sexton; Xiang Wan; Ivo D. Dinov; Brian D. Athey; Nicolas Rivron; Anne E. Carpenter; Beth A. Cimini; et al. (CoRR, 2025)